CA2927319C - Identification d'alleles a haute resolution - Google Patents

Identification d'alleles a haute resolution Download PDF

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Publication number
CA2927319C
CA2927319C CA2927319A CA2927319A CA2927319C CA 2927319 C CA2927319 C CA 2927319C CA 2927319 A CA2927319 A CA 2927319A CA 2927319 A CA2927319 A CA 2927319A CA 2927319 C CA2927319 C CA 2927319C
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alleles
map
hla
sequencing reads
locus
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CA2927319A1 (fr
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Yu Bai
Wen Fury
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Regeneron Pharmaceuticals Inc
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Regeneron Pharmaceuticals Inc
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    • G—PHYSICS
    • G16—INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
    • G16B—BIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
    • G16B20/00—ICT specially adapted for functional genomics or proteomics, e.g. genotype-phenotype associations
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
    • A61P43/00—Drugs for specific purposes, not provided for in groups A61P1/00-A61P41/00
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
    • C12Q1/68—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
    • C12Q1/6876—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes
    • C12Q1/6881—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for tissue or cell typing, e.g. human leukocyte antigen [HLA] probes
    • G—PHYSICS
    • G16—INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
    • G16B—BIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
    • G16B20/00—ICT specially adapted for functional genomics or proteomics, e.g. genotype-phenotype associations
    • G16B20/20—Allele or variant detection, e.g. single nucleotide polymorphism [SNP] detection
    • G—PHYSICS
    • G16—INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
    • G16B—BIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
    • G16B20/00—ICT specially adapted for functional genomics or proteomics, e.g. genotype-phenotype associations
    • G16B20/40—Population genetics; Linkage disequilibrium
    • G—PHYSICS
    • G16—INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
    • G16B—BIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
    • G16B30/00—ICT specially adapted for sequence analysis involving nucleotides or amino acids
    • G—PHYSICS
    • G16—INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
    • G16B—BIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
    • G16B30/00—ICT specially adapted for sequence analysis involving nucleotides or amino acids
    • G16B30/20—Sequence assembly
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q2600/00—Oligonucleotides characterized by their use
    • C12Q2600/156—Polymorphic or mutational markers

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  • Life Sciences & Earth Sciences (AREA)
  • Health & Medical Sciences (AREA)
  • Physics & Mathematics (AREA)
  • Chemical & Material Sciences (AREA)
  • Engineering & Computer Science (AREA)
  • Bioinformatics & Cheminformatics (AREA)
  • Proteomics, Peptides & Aminoacids (AREA)
  • Analytical Chemistry (AREA)
  • General Health & Medical Sciences (AREA)
  • Biophysics (AREA)
  • Biotechnology (AREA)
  • Genetics & Genomics (AREA)
  • Theoretical Computer Science (AREA)
  • Spectroscopy & Molecular Physics (AREA)
  • Medical Informatics (AREA)
  • Evolutionary Biology (AREA)
  • Bioinformatics & Computational Biology (AREA)
  • Molecular Biology (AREA)
  • Organic Chemistry (AREA)
  • Wood Science & Technology (AREA)
  • Zoology (AREA)
  • Immunology (AREA)
  • Cell Biology (AREA)
  • Biochemistry (AREA)
  • General Engineering & Computer Science (AREA)
  • Microbiology (AREA)
  • Physiology (AREA)
  • Ecology (AREA)
  • Animal Behavior & Ethology (AREA)
  • General Chemical & Material Sciences (AREA)
  • Chemical Kinetics & Catalysis (AREA)
  • Veterinary Medicine (AREA)
  • Public Health (AREA)
  • Pharmacology & Pharmacy (AREA)
  • Nuclear Medicine, Radiotherapy & Molecular Imaging (AREA)
  • Medicinal Chemistry (AREA)
  • Measuring Or Testing Involving Enzymes Or Micro-Organisms (AREA)
  • Materials For Medical Uses (AREA)
  • Medicines Containing Material From Animals Or Micro-Organisms (AREA)
  • Micro-Organisms Or Cultivation Processes Thereof (AREA)

Abstract

La présente invention concerne des procédés de détermination précise des allèles présents au niveau d'un locus qui est largement applicable à n'importe quel locus, comprenant des loci hautement polymorphiques, tels que des loci HLA, des loci BGA et des loci HV. Des modes de réalisation des procédés de l'invention sont utiles dans une large gamme d'applications, comprenant, par exemple, la greffe d'organe, les médicaments personnalisés, les diagnostics, les sciences judiciaires et l'anthropologie.
CA2927319A 2013-10-15 2014-10-14 Identification d'alleles a haute resolution Active CA2927319C (fr)

Applications Claiming Priority (3)

Application Number Priority Date Filing Date Title
US201361891193P 2013-10-15 2013-10-15
US61/891,193 2013-10-15
PCT/IB2014/002843 WO2015056103A2 (fr) 2013-10-15 2014-10-14 Identification d'allèles à haute résolution

Publications (2)

Publication Number Publication Date
CA2927319A1 CA2927319A1 (fr) 2015-04-23
CA2927319C true CA2927319C (fr) 2023-03-28

Family

ID=52630401

Family Applications (1)

Application Number Title Priority Date Filing Date
CA2927319A Active CA2927319C (fr) 2013-10-15 2014-10-14 Identification d'alleles a haute resolution

Country Status (8)

Country Link
US (2) US10162933B2 (fr)
EP (1) EP3058095B1 (fr)
JP (2) JP6491651B2 (fr)
KR (1) KR102386134B1 (fr)
CN (1) CN106103736B (fr)
AU (1) AU2014335877B2 (fr)
CA (1) CA2927319C (fr)
WO (1) WO2015056103A2 (fr)

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US9116866B2 (en) 2013-08-21 2015-08-25 Seven Bridges Genomics Inc. Methods and systems for detecting sequence variants
US9898575B2 (en) 2013-08-21 2018-02-20 Seven Bridges Genomics Inc. Methods and systems for aligning sequences
EP3058095B1 (fr) 2013-10-15 2019-12-25 Regeneron Pharmaceuticals, Inc. Identification d'allèles à haute résolution
EP3058093B1 (fr) 2013-10-18 2019-07-17 Seven Bridges Genomics Inc. Méthodes et systèmes d'identification de mutations induites par une maladie
KR20160062763A (ko) 2013-10-18 2016-06-02 세븐 브릿지스 지노믹스 인크. 유전자 샘플을 유전자형 결정하기 위한 방법 및 시스템
US10832797B2 (en) 2013-10-18 2020-11-10 Seven Bridges Genomics Inc. Method and system for quantifying sequence alignment
US11049587B2 (en) 2013-10-18 2021-06-29 Seven Bridges Genomics Inc. Methods and systems for aligning sequences in the presence of repeating elements
US9092402B2 (en) 2013-10-21 2015-07-28 Seven Bridges Genomics Inc. Systems and methods for using paired-end data in directed acyclic structure
WO2015085350A1 (fr) * 2013-12-10 2015-06-18 Conexio Genomics Pty Ltd Procédés et sondes pour identifier des allèles géniques
WO2015105963A1 (fr) 2014-01-10 2015-07-16 Seven Bridges Genomics Inc. Systèmes et procédés d'utilisation d'allèles connus en cartographie de lectures
US9817944B2 (en) 2014-02-11 2017-11-14 Seven Bridges Genomics Inc. Systems and methods for analyzing sequence data
WO2016141294A1 (fr) 2015-03-05 2016-09-09 Seven Bridges Genomics Inc. Systèmes et procédés d'analyse de motifs génomiques
US10793895B2 (en) 2015-08-24 2020-10-06 Seven Bridges Genomics Inc. Systems and methods for epigenetic analysis
MX2018002293A (es) 2015-08-25 2018-09-05 Nantomics Llc Sistemas y métodos para las llamadas variantes de alta precisión.
US10724110B2 (en) 2015-09-01 2020-07-28 Seven Bridges Genomics Inc. Systems and methods for analyzing viral nucleic acids
US10584380B2 (en) 2015-09-01 2020-03-10 Seven Bridges Genomics Inc. Systems and methods for mitochondrial analysis
WO2017058904A1 (fr) * 2015-09-28 2017-04-06 Sirona Genomics, Inc. Base de données et procédé de déséquilibre de liaison
US11347704B2 (en) 2015-10-16 2022-05-31 Seven Bridges Genomics Inc. Biological graph or sequence serialization
KR101651817B1 (ko) 2015-10-28 2016-08-29 대한민국 Ngs 라이브러리 제작용 프라이머 세트 및 이를 이용한 ngs 라이브러리 제작방법 및 키트
US20170199960A1 (en) 2016-01-07 2017-07-13 Seven Bridges Genomics Inc. Systems and methods for adaptive local alignment for graph genomes
US10364468B2 (en) 2016-01-13 2019-07-30 Seven Bridges Genomics Inc. Systems and methods for analyzing circulating tumor DNA
US10262102B2 (en) 2016-02-24 2019-04-16 Seven Bridges Genomics Inc. Systems and methods for genotyping with graph reference
US10790044B2 (en) 2016-05-19 2020-09-29 Seven Bridges Genomics Inc. Systems and methods for sequence encoding, storage, and compression
CA3022851A1 (fr) * 2016-05-27 2017-11-30 Human Longevity, Inc. Methodes de typage de l'antigene leucocytaire humain
WO2017218864A1 (fr) * 2016-06-17 2017-12-21 Mayo Foundation For Medical Education And Research Procédés et matériaux pour l'utilisation efficace de l'enrichissement ciblé combiné de régions génomiques et du séquençage de génome entier à faible chevauchement
KR101815529B1 (ko) * 2016-07-29 2018-01-30 (주)신테카바이오 휴먼 하플로타이핑 시스템 및 방법
US11289177B2 (en) 2016-08-08 2022-03-29 Seven Bridges Genomics, Inc. Computer method and system of identifying genomic mutations using graph-based local assembly
US11250931B2 (en) 2016-09-01 2022-02-15 Seven Bridges Genomics Inc. Systems and methods for detecting recombination
US11324801B2 (en) 2016-09-02 2022-05-10 University Of Utah Research Foundation NNIF and nNIF-related peptides and related methods
EP3516057A4 (fr) * 2016-09-26 2020-06-03 Sirona Genomics, Inc. Procédé de génotypage d'antigène leucocytaire humain et détermination de la diversité d'haplotype de hla dans une population d'échantillons
US10319465B2 (en) 2016-11-16 2019-06-11 Seven Bridges Genomics Inc. Systems and methods for aligning sequences to graph references
KR101936933B1 (ko) * 2016-11-29 2019-01-09 연세대학교 산학협력단 염기서열의 변이 검출방법 및 이를 이용한 염기서열의 변이 검출 디바이스
US20210265010A1 (en) * 2016-12-15 2021-08-26 Sirona Genomics, Inc. Genotyping diploid samples with coverage plot of unexplained reads
US11347844B2 (en) 2017-03-01 2022-05-31 Seven Bridges Genomics, Inc. Data security in bioinformatic sequence analysis
US10726110B2 (en) 2017-03-01 2020-07-28 Seven Bridges Genomics, Inc. Watermarking for data security in bioinformatic sequence analysis
CA3068203A1 (fr) 2017-07-14 2019-01-17 The Francis Crick Institute Limited Analyse d'alleles hla dans des tumeurs et utilisations associees
KR102035615B1 (ko) * 2017-08-07 2019-10-23 연세대학교 산학협력단 유전자 패널에 기초한 염기서열의 변이 검출방법 및 이를 이용한 염기서열의 변이 검출 디바이스
WO2019050958A2 (fr) * 2017-09-06 2019-03-14 Nant Holdings Ip, Llc Correspondance de tissu hla et procédés associés
US12046325B2 (en) 2018-02-14 2024-07-23 Seven Bridges Genomics Inc. System and method for sequence identification in reassembly variant calling
US11819520B2 (en) 2018-02-23 2023-11-21 Duke University Cultured thymus tissue transplantation promotes donor-specific tolerance to allogeneic solid organ transplants
EP3755346A4 (fr) * 2018-02-23 2022-03-09 Duke University & Medical Center Greffe de tissus de thymus cultivés favorisant une tolérance spécifique au donneur à des greffons d'organes solides allogéniques
CN109448789A (zh) * 2018-09-17 2019-03-08 上海派森诺生物科技股份有限公司 一种基于perl语言的种群特异SNP位点的自动化分析方法
CN110942806A (zh) * 2018-09-25 2020-03-31 深圳华大法医科技有限公司 一种血型基因分型方法和装置及存储介质
JP2022534071A (ja) * 2019-05-22 2022-07-27 ソウル ナショナル ユニバーシティ アールアンドディービー ファウンデーション Ｎｇｓデータを用いて遺伝型を予測する方法及び装置
CN111312332B (zh) * 2020-02-13 2020-10-30 国家卫生健康委科学技术研究所 基于hla基因的生物信息处理方法、装置及终端
WO2023196925A2 (fr) * 2022-04-07 2023-10-12 Guardant Health, Inc. Méthodes et systèmes de typage d'allèles
WO2023225607A2 (fr) * 2022-05-18 2023-11-23 The University Of North Carolina At Chapel Hill Génotypage de hla amélioré par identifiant moléculaire unique et quantification de transcription à l'aide d'une technologie à nanopores
WO2024112946A1 (fr) * 2022-11-22 2024-05-30 University Of Southern California Test de méthylation de l'adn acellulaire pour le cancer du sein

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US20100256917A1 (en) * 2007-06-15 2010-10-07 Mcvean Gilean Allelic determination
CN104160391A (zh) * 2011-09-16 2014-11-19 考利达基因组股份有限公司 确定异质样本的基因组中的变异
EP3058095B1 (fr) 2013-10-15 2019-12-25 Regeneron Pharmaceuticals, Inc. Identification d'allèles à haute résolution

Also Published As

Publication number Publication date
US10162933B2 (en) 2018-12-25
AU2014335877A2 (en) 2016-06-16
US20150110754A1 (en) 2015-04-23
WO2015056103A3 (fr) 2016-01-21
US11594302B2 (en) 2023-02-28
AU2014335877A1 (en) 2016-05-05
CN106103736A (zh) 2016-11-09
JP2019145114A (ja) 2019-08-29
WO2015056103A2 (fr) 2015-04-23
AU2014335877B2 (en) 2020-09-17
JP2016541043A (ja) 2016-12-28
CN106103736B (zh) 2020-03-03
US20190121940A1 (en) 2019-04-25
KR20160063400A (ko) 2016-06-03
EP3058095A2 (fr) 2016-08-24
JP6491651B2 (ja) 2019-03-27
KR102386134B1 (ko) 2022-04-12
EP3058095B1 (fr) 2019-12-25
JP6715977B2 (ja) 2020-07-01
CA2927319A1 (fr) 2015-04-23

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